tbuckley/cabot-search huggingface dataset:
Key bacterial taxa determine longitudinal dynamics of aromatic amino acid catabolism in infants’ gut
Authors: Martin F. Laursen, Anurag K. Sinha, Mikael Pedersen, Henrik M. Roager
Journal: Gut Microbes (2023)

The development of the gut microbiota in early life is linked to metabolic, neuronal, and immunological development. Recent studies have shown that bacterial production of short-chain fatty acids (SCFAs) and aromatic amino acid (AAA) catabolites in the gut can mediate host–microbe interactions. However, the dynamics of these microbiota-derived metabolites and the key bacterial taxa producing AAA catabolites during infancy are largely unknown. Here, we investigated the longitudinal dynamics of the microbiota and microbiota-derived SCFAs and AAA catabolites in more than 200 fecal samples from 25 healthy breast- or mixed-fed Danish infants during the first 6 months of life. We found that the gut microbiota composition and metabolism were highly individual but showed significant development over time. SCFAs and specific groups of AAA catabolites showed distinct temporal abundance patterns. Furthermore, we identified bacterial taxa responsible for the generation of AAA catabolites by associating the dynamics of gut microbial taxa and AAA catabolites and subsequently validating these associations in vitro by cultivation of strains representing the associated taxa. In addition to specific Bifidobacterium species being the main producers of aromatic lactic acids, we identified Peptostreptococcus anaerobius as the main producer of aromatic propionic acids, Ruminococcus gnavus as a main producer of tryptamine, and Enterococcus species as main tyramine producers in infants' gut. Thus, our results showcase the temporal dynamics of key gut microbial metabolites in early life and demonstrate that the appearance and abundance of specific AAA catabolites result from the appearance and abundance of specific key bacterial taxa in infants' gut.
Supplemental Nutrition Assistance Program Access and Racial Disparities in Food Insecurity
Authors: Laura J. Samuel, Deidra C. Crews, Bonnielin K. Swenor, Jiafeng Zhu, Elizabeth A. Stuart, Sarah L. Szanton, Boeun Kim, Pallavi Dwivedi, Qiwei Li, Nicholas S. Reed, Roland J. Thorpe
Journal: JAMA Network Open (2023)

Importance Racially minoritized people experience disproportionately high rates of food insecurity. The Supplemental Nutrition Assistance Program (SNAP) reduces food insecurity. Objective To evaluate SNAP access with regard to racial disparities in food insecurity. Design, Setting, and Participants This cross-sectional study used data from the 2018 Survey of Income and Program Participation (SIPP). On the basis of random sampling strategies, 44 870 households were eligible for the SIPP, and 26 215 (58.4%) participated. Sampling weights accounted for survey design and nonresponse. Data were analyzed from February 25 to December 12, 2022. Exposures This study examined disparities based on household racial composition (entirely Asian, entirely Black, entirely White, and multiple races or multirace based on SIPP categories). Main Outcomes and Measures Food insecurity during the prior year was measured using the validated 6-item US Department of Agriculture Food Security Survey Module. SNAP participation during the prior year was classified based on whether anyone in the household received SNAP benefits. Modified Poisson regression tested hypothesized disparities in food insecurity. Results A total of 4974 households that were eligible for SNAP (income ≤130% of the poverty threshold) were included in this study. A total of 218 households (5%) were entirely Asian, 1014 (22%) were entirely Black, 3313 (65%) were entirely White, and 429 (8%) were multiracial or of other racial groups. Adjusting for household characteristics, households that were entirely Black (prevalence rate [PR], 1.18; 95% CI, 1.04-1.33) or multiracial (PR, 1.25; 95% CI, 1.06-1.46) were more likely to be food insecure than entirely White households, but associations differed depending on SNAP participation. Among households that did not participate in SNAP, those that were entirely Black (PR, 1.52; 97.5% CI, 1.20-1.93) or multiracial (PR, 1.42; 97.5% CI, 1.04-1.94) were more likely to be food insecure than White households; however, among SNAP participants, Black households were less likely than White households to be food insecure (PR, 0.84; 97.5% CI, 0.71-0.99). Conclusions and Relevance In this cross-sectional study, racial disparities in food insecurity were found among low-income households that do not participate in SNAP but not among those that do, suggesting that access to SNAP should be improved. These results also highlight the need to examine the structural and systemic racism in food systems and in access to food assistance that may contribute to disparities.
Implications of Genetic Variants in Cerebral Palsy
Authors: Mark I. Evans, David W. Britt, Lawrence D. Devoe
Journal: JAMA Pediatrics (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Pediatrics HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Pediatrics journal
Microbiome-targeting therapies in the neonatal intensive care unit: safety and efficacy
Authors: Anna DeVeaux, Jian Ryou, Gautam Dantas, Barbara B. Warner, Phillip I. Tarr
Journal: Gut Microbes (2023)

Microbiome-targeting therapies have received great attention as approaches to prevent disease in infants born preterm, but their safety and efficacy remain uncertain. Here we summarize the existing literature, focusing on recent meta-analyses and systematic reviews that evaluate the performance of probiotics, prebiotics, and/or synbiotics in clinical trials and studies, emphasizing interventions for which the primary or secondary outcomes were prevention of necrotizing enterocolitis, late-onset sepsis, feeding intolerance, and/or reduction in hospitalization length or all-cause mortality. Current evidence suggests that probiotics and prebiotics are largely safe but conclusions regarding their effectiveness in the neonatal intensive care unit have been mixed. To address this ambiguity, we evaluated publications that collectively support benefits of probiotics with moderate to high certainty evidence in a recent comprehensive network meta-analysis, highlighting limitations in these trials that make it difficult to support with confidence the routine, universal administration of probiotics to preterm infants.
Changes in Registration Parameters for Ongoing Clinical Trials in Ukraine After 2022 Russian Invasion
Authors: Diana Gujinović, Tomislav Viđak, Mariia Melnikova, Nelson Joaquim Fortuna de Sousa, Ana Marušić
Journal: JAMA Network Open (2023)

Importance Clinical trial activity in Ukraine was seriously affected by the Russian invasion. However, data are lacking on how this conflict affects clinical trials. Objective To evaluate whether registered changes to trial information reflect war-related disturbances to trials in Ukraine. Design, Setting, and Participants This cross-sectional study included noncompleted trials conducted in Ukraine from February 24, 2022, to February 24, 2023. Trials conducted in Estonia and Slovakia were also analyzed for comparison. Study records within the ClinicalTrials.gov archive were accessed by using the change history feature in the tabular view for each record. Exposure Russian invasion of Ukraine. Main Outcomes and Measures The frequency of changes to the protocol and results registration parameters before and after the start of the war, February 24, 2022. Results A total of 888 ongoing trials conducted only in Ukraine (5.2%) or in multiple countries (94.8%), and enrolling a median of 348 participants were analyzed. Almost all sponsors for 775 industry-funded trials were non-Ukrainian (99.6%). On February 24, 2023, 267 trials (30.1%) were without any recorded update in the registry after the war. In 15 (1.7%) multisite trials, Ukraine was removed as a location country after mean (SD) of 9.4 (3.0) postwar months. The rates of changes in 20 parameters 1 year before and after the war started had a mean (SD) absolute difference of 3.0% (2.5%). Besides study status changes in each study record version, the contacts and locations field was the most frequently modified (56.1%), with a higher rate for multisite (58.2%) than in only Ukrainian (17.4%) trials. This finding was consistent for all analyzed registration parameters. In trials conducted solely in Ukraine, the median number of record versions was the year before (95% CI, 0-0) and after February 2022 (95% CI, 0-1), similar to registered trials from Estonia and Slovakia. Conclusions and Relevance Results of this study suggest that war-related changes in trial conduct in Ukraine may not be completely visible in the largest public trial registry, which is expected to present accurate and timely information on clinical trials. These findings raise questions regarding the updating practices for registration information, which should be mandatory, especially in times of crises, to ensure the safety and the rights of trial participants in a war zone.
Does the SCOUT Trial Fall Short of Determining an Effective Treatment Duration for Pediatric Urinary Tract Infections?
Authors: Aaron M. Milstone, Pranita D. Tamma
Journal: JAMA Pediatrics (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Pediatrics HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Pediatrics journal
L-arginine metabolism as pivotal interface of mutual host–microbe interactions in the gut
Authors: Björn Nüse, Tim Holland, Manfred Rauh, Roman G. Gerlach, Jochen Mattner
Journal: Gut Microbes (2023)

L-arginine (L-arg) is a versatile amino acid and a central intestinal metabolite in mammalian and microbial organisms. Thus, L-arg participates as precursor of multiple metabolic pathways in the regulation of cell division and growth. It also serves as a source of carbon, nitrogen, and energy or as a substrate for protein synthesis. Consequently, L-arg can simultaneously modify mammalian immune functions, intraluminal metabolism, intestinal microbiota, and microbial pathogenesis. While dietary intake, protein turnover or de novo synthesis usually supply L-arg in sufficient amounts, the expression of several key enzymes of L-arg metabolism can change rapidly and dramatically following inflammation, sepsis, or injury. Consequently, the availability of L-arg can be restricted due to increased catabolism, transforming L-arg into an essential amino acid. Here, we review the enzymatic pathways of L-arg metabolism in microbial and mammalian cells and their role in immune function, intraluminal metabolism, colonization resistance, and microbial pathogenesis in the gut.
Patient navigation across the cancer care continuum: An overview of systematic reviews and emerging literature
Authors: Raymond J. Chan, Vivienne E. Milch, Fiona Crawford‐Williams, Oluwaseyifunmi Andi Agbejule, Ria Joseph, Jolyn Johal, Narayanee Dick, Matthew P. Wallen, Julie Ratcliffe, Anupriya Agarwal, Larissa Nekhlyudov, Matthew Tieu, Manaf Al‐Momani, Scott Turnbull, Rahul Sathiaraj, Dorothy Keefe, Nicolas H. Hart
Journal: CA A Cancer Journal for Clinicians (2023)

Patient navigation is a strategy for overcoming barriers to reduce disparities and to improve access and outcomes. The aim of this umbrella review was to identify, critically appraise, synthesize, and present the best available evidence to inform policy and planning regarding patient navigation across the cancer continuum. Systematic reviews examining navigation in cancer care were identified in the Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, Embase, Cumulative Index of Nursing and Allied Health (CINAHL), Epistemonikos, and Prospective Register of Systematic Reviews (PROSPERO) databases and in the gray literature from January 1, 2012, to April 19, 2022. Data were screened, extracted, and appraised independently by two authors. The JBI Critical Appraisal Checklist for Systematic Review and Research Syntheses was used for quality appraisal. Emerging literature up to May 25, 2022, was also explored to capture primary research published beyond the coverage of included systematic reviews. Of the 2062 unique records identified, 61 systematic reviews were included. Fifty-four reviews were quantitative or mixed-methods reviews, reporting on the effectiveness of cancer patient navigation, including 12 reviews reporting costs or cost-effectiveness outcomes. Seven qualitative reviews explored navigation needs, barriers, and experiences. In addition, 53 primary studies published since 2021 were included. Patient navigation is effective in improving participation in cancer screening and reducing the time from screening to diagnosis and from diagnosis to treatment initiation. Emerging evidence suggests that patient navigation improves quality of life and patient satisfaction with care in the survivorship phase and reduces hospital readmission in the active treatment and survivorship care phases. Palliative care data were extremely limited. Economic evaluations from the United States suggest the potential cost-effectiveness of navigation in screening programs.
Polycythemia vera: 2024 update on diagnosis, risk‐stratification, and management
Authors: Ayalew Tefferi, Tiziano Barbui
Journal: American Journal of Hematology (2023)

Abstract Disease Overview Polycythemia vera (PV) is a JAK2 ‐mutated myeloproliferative neoplasm characterized by clonal erythrocytosis; other features include leukocytosis, thrombocytosis, splenomegaly, pruritus, constitutional symptoms, microcirculatory disturbances, and increased risk of thrombosis and progression into myelofibrosis (post‐PV MF) or acute myeloid leukemia (AML). Diagnosis A working diagnosis is considered in the presence of a JAK2 mutation associated with hemoglobin/hematocrit levels of &gt;16.5 g/dL/49% in men or 16 g/dL/48% in women; morphologic confirmation by bone marrow examination is advised but not mandated. Cytogenetics Abnormal karyotype is seen in 15%–20% of patients with the most frequent sole abnormalities being +9 (5%), loss of chromosome Y (4%), +8 (3%), and 20q− (3%). Mutations Over 50% of patients harbor DNA sequence variants/mutations other than JAK2 , with the most frequent being TET2 (18%) and ASXL1 (15%). Prognostically adverse mutations include SRSF2, IDH2, RUNX1 , and U2AF1 , with a combined incidence of 5%–10%. Survival and Prognosis Median survival is ⁓15 years but exceeds 35 years for patients aged ≤40 years. Risk factors for survival include older age, leukocytosis, abnormal karyotype, and the presence of adverse mutations. Twenty‐year risk for thrombosis, post‐PV MF, or AML are ⁓26%, 16% and 4%, respectively. Risk Factors for Thrombosis Two risk categories are considered: high (age &gt;60 years or thrombosis history) and low (absence of both risk factors). Additional predictors for arterial thrombosis include cardiovascular risk factors and for venous thrombosis higher absolute neutrophil count and JAK2 V617F allele burden. Treatment Current goal of therapy is to prevent thrombosis. Periodic phlebotomy, with a hematocrit target of &lt;45%, combined with once‐ or twice‐daily aspirin (81 mg) therapy, absent contraindications, is the backbone of treatment in all patients, regardless of risk category. Cytoreductive therapy is reserved for high‐risk disease with first‐line drugs of choice being hydroxyurea and pegylated interferon‐α and second‐line busulfan and ruxolitinib. In addition, systemic anticoagulation is advised in patients with venous thrombosis history. Additional Treatment Considerations At the present time, we do not consider a drug‐induced reduction in JAK2 V617F allele burden, which is often incomplete and seen not only with peg‐IFN but also with ruxolitinib and busulfan, as an indicator of disease‐modifying activity, unless accompanied by cytogenetic and independently‐verified morphologic remission. Accordingly, we do not use the specific parameter to influence treatment choices. The current review also includes specific treatment strategies in the context of pregnancy, splanchnic vein thrombosis, pruritus, perioperative care, and post‐PV MF.
Affect, Values and Problems Assessing Decision-Making Capacity
Authors: Jennifer Hawkins
Journal: The American Journal of Bioethics (2023)

The dominant approach to assessing decision-making capacity in medicine focuses on determining the extent to which individuals possess certain core cognitive abilities. Critics have argued that this model delivers the wrong verdict in certain cases where patient values that are the product of mental disorder or disordered affective states undermine decision-making without undermining cognition. I argue for a re-conceptualization of what it is to possess the capacity to make medical treatment decisions. It is, I argue, the ability to track one's own personal interests at least as well as most people can. Using this idea, I demonstrate that it is possible to craft a solution for the problem cases—one that neither alters existing criteria in dangerous ways (e.g. does not open the door to various kinds of abuse) nor violates the spirit of widely accepted ethical constraints on decision-making assessment.
Domestic Violence Housing First Model and Association With Survivors’ Housing Stability, Safety, and Well-being Over 2 Years
Authors: Cris M. Sullivan, Cortney Simmons, Mayra Guerrero, Adam Farero, Gabriela López-Zerón, Oyesola Oluwafunmilayo Ayeni, Danielle Chiaramonte, Mackenzie Sprecher, Aileen I. Fernandez
Journal: JAMA Network Open (2023)

Intimate partner violence (IPV) is a leading cause of homelessness and a serious threat to public health and well-being.
Dead rats, dopamine, performance metrics, and peacock tails: Proxy failure is an inherent risk in goal-oriented systems
Authors: Yohan J. John, Leigh Caldwell, Dakota E. McCoy, Oliver Braganza
Journal: Behavioral and Brain Sciences (2023)

Abstract When a measure becomes a target, it ceases to be a good measure. For example, when standardized test scores in education become targets, teachers may start “teaching to the test,” leading to breakdown of the relationship between the measure – test performance – and the underlying goal – quality education. Similar phenomena have been named and described across a broad range of contexts, such as economics, academia, machine learning, and ecology. Yet it remains unclear whether these phenomena bear only superficial similarities, or if they derive from some fundamental unifying mechanism. Here, we propose such a unifying mechanism, which we label proxy failure . We first review illustrative examples and their labels, such as the “cobra effect,” “Goodhart's law,” and “Campbell's law.” Second, we identify central prerequisites and constraints of proxy failure, noting that it is often only a partial failure or divergence . We argue that whenever incentivization or selection is based on an imperfect proxy measure of the underlying goal, a pressure arises that tends to make the proxy a worse approximation of the goal. Third, we develop this perspective for three concrete contexts, namely neuroscience, economics, and ecology, highlighting similarities and differences. Fourth, we outline consequences of proxy failure, suggesting it is key to understanding the structure and evolution of goal-oriented systems. Our account draws on a broad range of disciplines, but we can only scratch the surface within each. We thus hope the present account elicits a collaborative enterprise, entailing both critical discussion as well as extensions in contexts we have missed.
Scoping Review of Published Oncology Meta-analyses in High-Impact Oncology Journals
Authors: Alyson Haslam, Jordan Tuia, Vinay Prasad
Journal: JAMA Network Open (2023)

Importance Many meta-analyses have been conducted on a wide array of topics, and many of these have focused on treatment efficacy of drugs or bias in interventional studies on a specific topic. Objective To examine the factors associated with having a positive study conclusion in meta-analyses in the field of oncology. Evidence Review All meta-analyses published between January 1, 2018, and December 31, 2021, on 5 oncology journal websites were identified and study characteristics, study results, and information on study authors were abstracted. The meta-analysis authors’ conclusions were coded as positive, negative, or equivocal, and each article subject matter was coded as one that could affect profits and marketing of a company. Whether an association existed between study characteristics and authors’ conclusions was also examined. Findings Database searches resulted in 3947 potential articles, of which 93 meta-analyses were included in this study. Of the 21 studies with author funding from industry, 17 studies (81.0%) reported favorable conclusions. Of the 9 studies that received industry funding, 7 (77.8%) reported favorable conclusions, and of the 63 studies that did not have author or study funding from industry, 30 (47.6%) reported favorable conclusions. Studies that were funded through nonindustry sources and authors who had no relevant conflict of interest had the lowest percentage of positive conclusions and the highest percentage of negative and equivocal conclusions compared with studies with other sources of potential conflict of interest. Conclusions and Relevance In this cross-sectional study of meta-analyses published in oncology journals, multiple factors were associated with having a positive study conclusion, which suggests that future research should be performed to elucidate reasons for more favorable conclusions among studies with study or author industry funding.
Characteristics Associated With Cannabis Use Initiation by Late Childhood and Early Adolescence in the Adolescent Brain Cognitive Development (ABCD) Study
Authors: Alex P. Miller, David A. A. Baranger, Sarah E. Paul, Alexander S. Hatoum, Cynthia Rogers, Ryan Bogdan, Arpana Agrawal
Journal: JAMA Pediatrics (2023)

This cohort study evaluates characteristics associated with early-onset cannabis use.